We began with a set of 20 archival stage II–III primary HER2-positive breast tumors that were treated with neoadjuvant chemotherapy combined with HER2-targeted therapy: for each, we performed whole-exome sequencing on one pre-treatment region (from the diagnostic core needle biopsy), one post-treatment region (from the surgical specimen), and matched normal tissue (from the surgical specimen). The gene discussed is ERBB2; the disease is breast neoplasm.